Index

A

AMI() (in module episcanpy.api.tl)

ARI() (in module episcanpy.api.tl)

B

binarize() (in module episcanpy.api.pp)

bld_mtx_fly() (in module episcanpy.api.ct) build_count_mtx() (in module episcanpy.api.ct)

C

cal_var() (in module episcanpy.api.pl) (in module episcanpy.api.pp) cluster_composition() (in module episcanpy.api.pl) clustermap() (in module episcanpy.api.pl)

commonness_features() (in module episcanpy.api.pp) correlation_matrix() (in module episcanpy.api.pl) correlation_pc() (in module episcanpy.api.pp) coverage_cells() (in module episcanpy.api.pp) coverage_features() (in module episcanpy.api.pp)

D

dendogram() (in module episcanpy.api.tl) dendrogram() (in module episcanpy.api.pl) density_features() (in module episcanpy.api.pp) diffmap() (in module episcanpy.api.pl) (in module episcanpy.api.tl)

dotplot() (in module episcanpy.api.pl) downsample_counts() (in module episcanpy.api.pp) dpt() (in module episcanpy.api.tl) draw_graph() (in module episcanpy.api.pl) (in module episcanpy.api.tl)

E

episcanpy module

F

filter_cells() (in module episcanpy.api.pp)

filter_features() (in module episcanpy.api.pp)

G

geneactivity() (in module episcanpy.api.tl)

getNClusters() (in module episcanpy.api.tl)

H

hc() (in module episcanpy.api.tl)

heatmap() (in module episcanpy.api.pl) homogeneity() (in module episcanpy.api.tl)

I

identify_cluster() (in module episcanpy.api.tl)

imputation_met() (in module episcanpy.api.pp)

K

kmeans() (in module episcanpy.api.tl)

L

lazy() (in module episcanpy.api.pp) (in module episcanpy.api.tl) leiden() (in module episcanpy.api.tl) load_features() (in module episcanpy.api.ct) load_markers() (in module episcanpy.api.tl)

load_met_noimput() (in module episcanpy.api.ct) (in module episcanpy.api.pp) load_metadata() (in module episcanpy.api.pp) log1p() (in module episcanpy.api.pp) louvain() (in module episcanpy.api.tl)

M

make_windows() (in module episcanpy.api.ct) matrixplot() (in module episcanpy.api.pl)

module episcanpy

N

name_features() (in module episcanpy.api.ct) neighbors() (in module episcanpy.api.pp)

normalize_per_cell() (in module episcanpy.api.pp) normalize_total() (in module episcanpy.api.pp)

O

overlap_heatmap() (in module episcanpy.api.pl)

P

pca() (in module episcanpy.api.pl) (in module episcanpy.api.pp) pca_loadings() (in module episcanpy.api.pl)

pca_overview() (in module episcanpy.api.pl) pca_variance_ratio() (in module episcanpy.api.pl) plot_size_features() (in module episcanpy.api.ct) prct_overlap() (in module episcanpy.api.pl)

R

rank_feat_groups() (in module episcanpy.api.pl) rank_feat_groups_dotplot() (in module episcanpy.api.pl) rank_feat_groups_heatmap() (in module episcanpy.api.pl) rank_feat_groups_matrixplot() (in module episcanpy.api.pl) rank_feat_groups_stacked_violin() (in module episcanpy.api.pl) rank_feat_groups_tracksplot() (in module episcanpy.api.pl)

rank_feat_groups_violin() (in module episcanpy.api.pl) rank_features() (in module episcanpy.api.tl) ranking() (in module episcanpy.api.pl) read_ATAC_10x() (in module episcanpy.api.pp) read_cyt_summary() (in module episcanpy.api.ct) readandimputematrix() (in module episcanpy.api.pp) regress_out() (in module episcanpy.api.pp)

S

save_sparse_mtx() (in module episcanpy.api.ct) scatter() (in module episcanpy.api.pl) select_var_feature() (in module episcanpy.api.pp) silhouette() (in module episcanpy.api.pl) (in module episcanpy.api.tl)

silhouette_tot() (in module episcanpy.api.pl) size_feature_norm() (in module episcanpy.api.ct) sparse() (in module episcanpy.api.pp) stacked_violin() (in module episcanpy.api.pl) subsample() (in module episcanpy.api.pp)

T

top_feature_genes() (in module episcanpy.api.tl) tracksplot() (in module episcanpy.api.pl)

tsne() (in module episcanpy.api.pl) (in module episcanpy.api.tl)

U

umap() (in module episcanpy.api.pl) (in module episcanpy.api.tl)

V

var_features_to_genes() (in module episcanpy.api.tl) variability_features() (in module episcanpy.api.pl) (in module episcanpy.api.pp)

violin() (in module episcanpy.api.pl)